Structural and antigenic variations in the spike protein of emerging SARS-CoV-2 variants

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus is continuously evolving, and this poses a major threat to antibody therapies and currently authorized Coronavirus Disease 2019 (COVID-19) vaccines. It is therefore of utmost importance to investigate and predict the putative mutations on the spike protein that confer immune evasion. Antibodies are key components of the human immune system’s response to SARS-CoV-2, and the spike protein is a prime target of neutralizing antibodies (nAbs) as it plays critical roles in host cell recognition, fusion, and virus entry. The potency of therapeutic antibodies and vaccines partly depends on how readily the virus can escape neutralization. Recent structural and functional studies have mapped the epitope landscape of nAbs on the spike protein, which illustrates the footprints of several nAbs and the site of escape mutations. In this review, we discuss (1) the emerging SARS-CoV-2 variants; (2) the structural basis for antibody-mediated neutralization of SARS-CoV-2 and nAb classification; and (3) identification of the RBD escape mutations for several antibodies that resist antibody binding and neutralization. These escape maps are a valuable tool to predict SARS-CoV-2 fitness, and in conjunction with the structures of the spike-nAb complex, they can be utilized to facilitate the rational design of escape-resistant antibody therapeutics and vaccines.


Introduction
Enveloped viruses are found across diverse viral families and are characterized by having a lipid bilayer (envelope) derived from the host cell membrane, which contains virus-encoded membrane protein (M), envelope protein (E), and glycoprotein peplomer or commonly known as spike protein (S). These peplomers are often seen as projections from the outer surface of the envelope and are essential for host cell recognition, fusion, and virus entry [1]. The spike glycoprotein is the dominant exposed antigen on enveloped viruses, which can trigger a series of adaptive immune responses mediated by 3 major cell types: B cells (humoral immunity) and CD4 + and CD8 + T cells (cell-mediated immunity) [1,2]. B cells activation in response to viral infection results in the production of antigen-specific antibodies that can neutralize and clear the virus particle. Viruses also develop immune evasion strategies for escaping these responses through several ways, such as antigenic shielding by the addition of complex glycans [3,4], by secreting truncated viral glycoproteins that share viral spike epitopes for subverting the host immune response [5], by antigenic variations [6], and by blocking complement activation and neutralization of virus particles [6]. On the other hand, activated B cells within germinal centers of secondary lymphoid organs produce class-switched memory B cells, which undergo rounds of population expansion, somatic hypermutation, and selection for improved antigen binding. These evolutionary strategies are regularly used by our immune system to protect us against virus variants and other pathogens [7][8][9]. In the ongoing Coronavirus Disease 2019 (COVID-19) pandemic, we are witnessing all these features of the human immune system along with continuously emerging Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants. The COVID-19 pandemic caused by the SARS-CoV-2 virus has claimed over 5 million lives worldwide since the first reported case in Wuhan, China [10,11]. Each SARS-CoV-2 contains 24 to 40 randomly arranged spike-like projections on its surface [12,13], which resemble a solar corona under the electron microscope, from which they get their name and are referred to as coronaviruses. The SARS-CoV-2 spike glycoprotein is a homotrimer composed of S1 and S2 subunits separated by a furin cleavage site (RRAR) that modulates its fusogenic activity [14]. The receptor-binding domain (RBD) and N-terminal domain (NTD) of the S1 subunit guide the SARS-COV-2 attachment to host cells, and the S2 subunit drives fusion between virus and host cell membrane [15][16][17][18]. Cryo-EM studies have indicated that the SARS-CoV-2 spike protein is wildly flexible and it exhibits several prefusion conformations where 3 RBDs adopt distinct orientations: "up" (receptor-accessible state) and "down" (receptor-inaccessible). Protomers with the up-conformation can facilitate the binding between the spike protein and the angiotensin-converting enzyme 2 (ACE2AU : PleasenotethatACE2hasbeendefinedasangiotensi antibodies [37][38][39][40][41]. In this review, we discuss the molecular characteristics of naturally occurring SARS-CoV-2 variants including the Delta and Omicron variants that armor them for escaping the therapeutic antibodies, natural infections, or even current vaccines. We define the structural analysis and classification of the RBD targeting antibodies to understand the molecular mechanisms of neutralization and potency differences among them. We further describe the identification of the RBD escape mutations for several antibodies that resist vaccine-elicited and therapeutically relevant antibodies binding with a focus on the SARS-CoV-2 variants.

SARS-CoV-2 variant classifications and definitions
All viruses acquire mutations as they evolve, and most mutations have either deleterious or neutral effects on viral fitness. However, certain amino acid substitutions, insertions, and deletions give the viruses a selective advantage, which potentially makes them more infectious, transmittable, and, ultimately, the dominant strain. This indicates that negative selection Spike protein structure shows the receptor-binding subunit S1 and the membrane-fusion subunit S2 separated by the furin-like protease site (S1/S2). Different subdomains of the spike protein are the NTD in green, RBD in gray containing RBM in cyan at their top, the fusion peptide in pink, second cleavage site S2' in red, and HR1 and HR2 in olive (PBB: 7BNN). The scissors represent the S1/S2 boundary at amino acid position 685. Left

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reduces genetic diversity and shapes the evolution of the virus, while positive selection affects only a small number of sites directly involved in the virus-host coevolution [42]. SARS-CoV-2 is no different and is quickly adapting to its new human host, and the first major step in this direction was a D614G mutation in the spike protein. In a short time, multiple structural and biochemical studies demonstrated that the virus harboring D614G mutation is more infectious than the Wuhan-Hu-1 isolate [43][44][45][46]. Since then, several genetic variants of SARS-CoV-2 have descended from it and spread around the world. The SARS-CoV-2 Interagency Group (SIG) in collaboration with the Centers for Disease Control and Prevention (CDC) has categorized 4 classes of SARS-CoV-2 variants, namely, variants being monitored (VBMs), variants of interest (VOIs), variants of concern (VOCs), and variants of high consequence (VOHCs) [ December 19, 2021. In the following section, we discuss the impacts of key mutations of selected VBMs and VOCs in the context of the structure and function of the spike protein.

Alpha
(B.1.1.7 lineage): This variant was first reported in the UK in September 2020, and since then, several countries have reported variants of this lineage. The characteristic features of this variant include Δ69/70 and Δ144 in the NTD and N501Y mutation in the RBD (Fig 2). Although the Δ69/70 in the NTD does not confer resistance to mAbs, it increases virus infectivity driven by higher levels of spike incorporation into virions. The Alpha variant induces faster syncytium formation that results in enhanced cell-cell fusion than the D614G variant [51]. Though N501 is one of the key residues that increases the RBD-ACE2 binding affinity [32,52], but the N501Y mutation has been shown to improve the binding affinity in vitro by hydrophobic interactions of the RBD Y501 with ACE2 Y41, and favorable cation-π stacking interactions with ACE2 K353 [21,53,54]. Overall, the mutations in the B.1.1.7 variant did not cause a major structural rearrangement in the RBD and NTD, which is apparent from a minimal change in the sensitivity of the Alpha variant to several potently neutralizing antibodies (nAbs). Among them, C63C8, C12A2, G32B6, C63C7 and C83B6, C81D6 are RBD and NTD targeting antibodies, respectively [54]. Taken together, it is concluded that the higher fusogenic potential [51] and improved fitness for replication in the upper airway [53] of the B.1.1.7 virus contribute to the higher mortality [55] and enhanced transmissibility [48,53]. Currently approved vaccines of Pfizer and AstraZeneca work against this variant with long-term efficacy comparable to that of D614G [56].

Beta
(B.1.351): This variant was first reported in Nelson Mandela Bay, South Africa, and since then, it has been reported in several countries including the USA. This variant has multiple mutations in the spike protein, including K417N, E484K, and N501Y, which were also seen in some of the Alpha variants; and amino acid deletions at 241-243 position (Fig 2). The Δ241-243 in the NTD (and Δ144 in B.1.1.7), N501Y, and E484K mutations are associated with reduced binding of certain nAbs and human serum antibodies [27,28,37,38,41,[57][58][59][60]. The triple-residue deletion in the NTD causes a shift of nearby loops designated as N3 (residues 144 to 155) and N5 (residues 246 to 260), which form part of the NTD neutralizing epitope [61] (see section 4.5). The E484K mutation results in increased electrostatic interactions at the RBD-ACE2 interface, and multiple studies have confirmed that the variants harboring E484K mutations in the RBD exhibit considerably stronger interactions to human ACE2 receptor [62][63][64], suggesting their contribution to a higher rate of transmission than previous variants (Fig 2). Recently, an in silico study has implicated weakening of the T and B cells interactions in the Beta variant, resulting in escape from immune surveillance [64]. Currently approved vaccines of Pfizer and AstraZeneca neutralize this variant with a reduced efficacy as compared to D614G and alpha [56].

Gamma
(P.1 lineage): This variant was first reported in Japan by 4 travelers from Brazil. This variant is a descendent of B.1.1.28 lineage. Though both Gamma and Beta variants possess similar mutations in the RBD (K417T/N, E484K, and N501Y), but the Gamma variant is surprisingly less resistant to naturally acquired or vaccine-induced antibodies than the Beta variant, suggesting that distantly located mutations appear to have an impact on neutralization [60]. For example, mAbs 5-24 and 4-8 (which target the same NTD-antigenic supersite as DH1050.1) lost neutralizing activity against B.1.351 but not P.1 [65]. Both Gama and Beta variants have multiple

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substitutions in the C-terminal of the spike protein with unknown significance (Fig 2). Currently approved vaccines work against this variant with rare events of breakthrough infections.  66], and since then, the Delta variant has spread around the world. This variant is specified by 11 mutations: T19R, T95I, G142D, Δ156-157, R158G, L452R, T478K, D614G, P681R, and D950N in the spike protein (Fig 2). Of these mutations, it has been observed that the P681R mutation is highly conserved in this lineage that facilitates the furin cleavage more efficiently, which drives enhanced fusogenicity and pathogenicity [66][67][68]. Interestingly, the Alpha variant, too, has a missense mutation at the amino acid position 681 with a histidine residue (P681H), but, interestingly, the Delta variant is about 60% more transmissible than the Alpha variant [24]. It has been observed that several mutations in the RBDs of these variants are located within and at the periphery of the ACE2-binding surface, suggesting that the virus accumulates mutations to avoid recognition by antibodies while maintaining binding to ACE2. For example, the L452R mutation in the Delta variant is located at the periphery of the ACE2-binding surface, which impairs neutralization by antibodies [69]. Instead of E484K, the Delta variant contains a unique mutation at a neighboring location, T478K, which facilitates immune escape due to a reduction or loss of binding by Class 1 and certain Class 2 nAbs [70]. The Delta and Omicron variants contain multiple mutations/deletions in the NTD supersite (see section 3.5.), which have not been observed in other major variants (Fig 2). These alterations result in reshaping the antigenic surface of the NTD loop (amino acid position 140-156) and a change in the glycan shield around the antigenic supersite, as indicated by the structural analysis of the Delta variant spike protein [21]. These modifications develop a total escape for the NTD-specific nAbs isolated from convalescent patient sera, infected with early Wuhanrelated strain, and a reduction in neutralization by vaccine-elicited sera [56].

Delta
SARS-CoV-2 vaccines based on the Wuhan-Hu-1 spike glycoprotein elicit a varied degrees of immune responses in individuals that have not previously been infected with SARS-CoV-2. With the Pfizer vaccine BNT162b2, it was observed that nAbs were low against the D614G variant and almost undetectable against the Alpha, Beta, and Delta variants. However, nAbs titres improved significantly after the second dose, and a 3-fold and 16-fold reduction in the neutralization titres were observed against the Delta and the Beta variants, respectively, when compared to the Alpha variant [66]. A similar trend was also noticed with the sera obtained from the AstraZeneca ChAdOx1 nCoV-19 vaccinated individuals [66]. Thus, both mRNA and adenoviral vector-based vaccines generate a neutralizing response that efficiently targets the SARS-CoV-2 variants only after the second dose.  (Fig 2). Some of the mutations in the spike protein of Omicron are known to increase transmissibility, and preliminary reports indicate that it is even more transmissible than the Delta variant [71,72]. For example, N501Y increases binding to the ACE2 receptor, which could increase transmission, and the combination of N501Y and Q498R may increase binding affinity even further. P681H has already been shown to enhance spike cleavage in the Alpha and Delta variants (P681R), and the Omicron variant contains 3 mutations (N679K, H655Y, and P681H) close to the furin cleavage site [25,73]. Planas and colleagues, in a recent study, found that among 9 mAbs in clinical use or in development, 6 (such as LY-CoV555, LY-CoV016, REGN-10933, REGN-10987, Tixagevimab, and Regdanvimab) lost antiviral activity against Omicron, while ADG-20 and Sotrovimab were less affected by the mutations in the Omicron variant with a half maximal inhibitory concentration (IC 50 ) of 1,114 and 391 ng/ml, respectively (Tables 1 and S1) [73]. They further observed that sera obtained from individuals receiving the Pfizer and Astra-Zeneca vaccines after 5 months of 2 doses displayed no antiviral activity against the Omicron variant [73]. However, Andrews and colleagues, in a recent study, reported that Pfizer-BioN-Tech vaccine retained approximately 37% of vaccine effectiveness after 15 weeks of 2 doses of Pfizer-BioNTech vaccine. Remarkably, the vaccine effectiveness increased to about 75% after third dose (also known as booster dose) of Pfizer-BioNTech vaccine [71]. Similar reports from Pfizer-BioNTech and Moderna press releases indicate that mRNA vaccines are still incredibly effective against the Omicron variant after the booster dose. Future studies with a large cohort of individuals and patients are needed to validate these findings, as well as to understand how different the Omicron is from the previously emerged SARS-CoV-2 variants.

Antibody responses to SARS-CoV-2 infection
The long-lasting antibody responses are the manifestation of coordinated interactions between the B and T cells within germinal centers of lymphoid organs. It is known that certain viral infections, such as smallpox, yellow fever, measles, and polio, confer long-lasting humoral and cell-mediated immunity, and most importantly, the virus-specific antibodies play a key role in providing long-term protection. However, after more than a year, the emergence of Table 1. Efficacy of clinical mAbs, lineages, and canonical mutations in SARS-CoV2 VOCs. REGN-CoV (REGN10987/Imdevimab and REGN10933/Casirivimab) by Regeneron, VIR-7832 and VIR-7831 (Sotrovimab) by GSK and Vir biotechnology, and LY-CoV555 (Bamlanivimab) and LY-CoV016 (Etesevimab) by Eli Lilly and Company are some of the approved antibody cocktails for emergency use in mild-to-moderate COVID-19 patients. These antibodies were obtained from the people who got infected with SARS-CoV-2 during the first wave of the pandemic. These therapeutic antibody cocktails targeting noncompeting epitopes have varied degrees of neutralizing efficacies against VOCs. The color of highlighted text represents the levels of efficacy mAb retains against each VOC: green represents the mAb retains efficacy; lightgreen represents reduced efficacy; and orange represents that the mAb is ineffective. ADG-20 developed by Adagio binds to an epitope located in between the Class 1 and Class 4 sites. https://doi.org/10.1371/journal.ppat.1010260.t001

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antigenically distinct SARS-CoV-2 variants has become a reality and a major concern for the effectiveness of currently used vaccines and mAb therapies. Antibodies prevent the pathology associated with productive infection mainly by 2 pathways: First, the Fab domain of an antibody binds specifically to a viral protein and blocks the ability of the virus to enter cells, a process referred to as neutralization. Second, the fragment crystallizable (Fc) portion of an IgG or IgM can induce cell lysis and death of virus-infected cells through a variety of immune effector mechanisms, including antibody-dependent cell-mediated cytotoxicity (ADCC), antibodydependent cellular phagocytosis (ADCP), and antibody-mediated complement activation [74][75][76] (Fig 3).
In a cohort of 647 SARS-CoV-2-infected patients from Italy, Switzerland, and the USA, Piccoli and colleagues observed that the antibody responses were mainly directed toward the spike and nucleocapsid proteins. They observed that the nucleocapsid protein-specific antibodies were not neutralizing, and about 90% of the neutralizing activity was mediated by the RBD-specific antibodies. The remaining neutralizing activity may be accounted for antibodies elicited against the S2 subunit and the NTDs [77]. Of note, the fusion machinery of the S2 subunit contains several antigenic sites and is more conserved than the S1 subunit, thus an attractive target for eliciting broadly neutralizing antibodies (bnAbs). These findings indicate that the lower level of glycosylation, multiple conformations that expose cryptic sites, and higher accessibility on the viral surface are some of the reasons behind the enhanced immunodominance of the RBDs. To understand the antigenic anatomy of the SARS-CoV-2 spike protein, and the molecular mechanism of SARS-CoV-2 neutralization mediated by numerous mAbs, several laboratories performed biophysical and structural studies of distinct COVID-19 nAbs in complex with the trimeric spike protein [70,[77][78][79][80][81][82][83]. This information has allowed the PLOS PATHOGENS classification of these antibodies into different categories. In brief, Hastie and colleagues analyzed the 186 RBD-reactive mAbs using a high-throughput surface plasmon resonance technique that broadly grouped RBD-directed mAbs into 7 discrete communities and functionally relevant subclusters. They further mapped the footprints of 25 RBD-reactive mAbs by negative stain electron microscopy. Combining these biophysical and structural data together, the 7 communities were referred to as RBD-1 to RBD-3, RBD-4 to RBD-5, and RBD-6 to RBD-7, which are discussed in the next sections [80]. Tong and colleagues and Yuan and colleagues have also independently identified 7 and 3 major categories of the antibodies, respectively [81,83]. Here, in this review, we will discuss the classification of antibodies based on whether they bind an overlapping footprint with the ACE2 receptor and recognize an open or closed or both states of the RBD on the spike protein [70].

Class 2 neutralizing antibodies: Direct ACE2 competition by binding "up" and "down" RBDs
Structures of Class 2 (or RBD-4) antibodies in complex with the spike protein have revealed that they recognize RBDs in the "up" and "down" conformations by binding toward the outer edge of the RBM, and their epitopes overlap the ACE2-binding site but less than Class 1 members (Fig 4B and 4G). The Class 2 antibodies are encoded by a variety of the VH3 gene segments and are characterized by a longer CDRH3 loop of 25 amino acids [70,84]. The C144-S complex structure (PDB: 7K90) revealed 3 C144 Fabs binding to 3 "down" RBDs on the spike protein, and likely locking the spike protein in a prefusion conformation by inserting the CDHR3 loop between 2 adjacent RBDs ( Fig 4H). Thus, it is plausible to speculate that the C144-mediated sealing of the spike protein in the prefusion conformation might prevent breathing in the RBDs that potentially restrict them to flip to the up-conformation, in which the spike protein can bind to the ACE2 receptor. Due to these characteristics, C144 is a potent nAb with an IC50 of <10 ng/ml and is in clinical development for prophylaxis [93].
However, contrary to C144 binding, the structures of C002 (encoded by VH3-30 and VK1-39 gene segment; 17 amino acids long CDRH3 loop) and C121 (encoded by VH1-2 and VL2-23 gene segment; 23 amino acids long CDRH3 loop) in complex with the spike protein showed 2 modes of interactions, where they appear to bind simultaneously to 2 RBDs, from adjacent protomers, in both "up" and "down" conformations by forming a quaternary epitope [70]. In brief, along the lines of C144, the C002 and C121 RBD epitopes are concentrated largely on the receptor-binding ridge through interactions with light-chain CDR loops and with the RBD flat face engaged with heavy-chain CDR loops (Fig 4G and 4H) [70].
Regardless of the orientations in the context of binding the spike protein, the C144, C121, and C002 epitopes overlap with the ACE2-binding site, suggesting that the neutralization mechanism involves direct competition with the ACE2 receptor.

Class 3 neutralizing antibodies: Bind outside the direct RBD-ACE2 interface in both "up" and "down" RBDs
Class 1 and 2 antibodies inhibit SARS-CoV-2 virus entry by physically blocking the ACE2binding motif; however, there are other conserved regions on the RBD that are away from the receptor binding site but are targeted by antibodies for achieving virus neutralization. Class 3 antibodies (or RBD-5) recognize conserved epitopes located on the opposite side of the receptor-binding motif, including the 443-450 loop, which is accessible in both the up and down RBD conformations (Figs 1C and 4I). Several antibodies, such as C135, C110, and C309, bind the RBDs in the up-as well as in the down-conformations (Fig 4J), and they mediate neutralization either by steric hindrance, locking and cross-linking the trimeric spike protein, or by Fc-mediated antibody effector functions [95]. The structures of Class 3 antibodies in complex with the spike protein exhibit that the cross-linking of adjacent RBDs is possible in certain cases [80]. Since these antibodies bind outside the receptor-binding site, therefore, they leave open the possibility of being an ideal partner with Class 1 or 2 antibodies in designing effective therapeutic cocktail therapy. REGN10987 and REGN10933 represent such a pair of antibodies, where both antibodies can simultaneously bind at different epitopes on the RBD. In brief, REGN10987 binds at the side of the receptor-binding motif, including the 443-450 loop, like C110, and REGN10933 binding overlap with the ACE2-binding site [85] (Fig 4K). Preclinical studies have confirmed that a cocktail of REGN10987 and REGN10933, referred to as REGN-COV2, shows enhanced clearance of virus and suppresses the rapid emergence of antibody resistance [31]. S309 is a class 3 antibody that was screened from the blood sample of a SARS-CoV-infected patient. It binds to a conserved epitope that has been termed by Piccoli and colleagues as site IV [77]. It potently neutralizes SARS-CoV, SARS-CoV-2, and SARSrelated coronavirus WIV-1 by binding to a conserved epitope containing a glycan (N343 in SARS-CoV-2) on the RBD. S309 has shown increased neutralization potencies in combination with weakly nAbs and additionally exhibited that antibody cocktail reduces the generation of escape mutants [95]. VIR-7831 and VIR-7832 are dual-action mAbs in clinical use, which are derived from the S309 antibody [96]. REGN-COV2 and VIR-7831/VIR-7832 both have received emergency use authorization (EUA) for the treatment of mild-to-moderate COVID-19 patients. Other mAbs and medical countermeasures, which have been thus far given EUA and are under development, are listed in Tables 1 and S1.

Neutralizing antibodies that target the N-terminal domain of the RBD
Although the RBD is an immunodominant part of the S protein, a small fraction of mAbs has been found binding to the NTDs, and a few of them exhibited neutralizing abilities against SARS-CoV-2 [61,94,[106][107][108]. Chi and colleagues isolated such an antibody, named 4A8, which does not block the interactions between ACE2 and S protein but exhibits high neutralization potency against the SARS-CoV-2 virus. The 4A8 Fab binding stabilizes the NTD of the S protein that facilitated the building of 5 NTD loops, which are designated as N1 (residues 14 to 26), N2 (residues 67 to 79), N3 (residues 141 to 156), N4 (residues 177 to 186), and N5 (residues 246 to 260). The cryo-EM structure revealed that the NTD of each protomer is bound with 4A8 Fab (PDB: 7C2L) (Fig 4R), where 4A8 heavy chain mostly participates in binding with the N3 and N5 loops residues in the NTD (Y145, H146, K147, K150, W152, R246, and W258) of the spike protein [61]. DH1048 (EMD: 22936), DH1049 (EMD: 22942), DH1050.1 (EMD: 22944 and 23277, PDB: 7LCN), DH1050.2 (EMD: 22945), and DH1051 (EMD: 22946) are other NTD-specific nAbs [109], all of which target the same epitope as 4A8. Suryadevara and colleagues found 2 NTD-targeting antibodies from COVID-19 convalescent plasma, COV2-2676 and COV2-2489, which neutralize SARS-CoV-2 by inhibiting a post-attachment step in the infection cycle [106]. Interestingly, Fab fragments of these antibodies could not neutralize infection but required either intact IgG or F(ab)2 version for optimal therapeutic protection, suggesting that a larger size of antibodies either sterically inhibit functional interactions crucial for the entry process or Fc effector functions are also required for optimal protection or both.
Although the molecular mechanism of NTD-specific antibodies mediated neutralization is still not fully understood, it has been observed that they inhibit cell-cell fusion and activate effector functions to protect Syrian hamsters from SARS-CoV-2 challenge [107]. Several naturally occurring variants including the Alpha, Beta, and Gamma variants exhibit mutations in the NTD supersite, and these substitutions completely abolish the neutralizing activities of various NTD-specific nAbs [21,38,65,107]. This is one of the reasons that the RBD continues to be the main route for the formation of therapeutic antibodies (Tables 1 and S1).

Spike mutations and immune escape
The SARS-CoV-2 virus is continuously undergoing antigenic evolution driven by positive selection for mutations in the spike protein, particularly in the RBD. Antibodies generated either by vaccination or natural infection have been rendered ineffective by some of these variants that are selected in infected individuals. The atomic structures of the spike protein and nAbs complexes undoubtedly define the protein-protein interaction interfaces that are known as "structural epitope"; however, they do not define sites where mutations will affect antibody binding and neutralization. These sites are often referred to as "functional binding epitopes" and are usually smaller than the "structural epitopes" [26, 112,113]. Several laboratories have generated functional maps of antigen-binding sites experimentally by different approaches but with the same goal [27][28][29][30]33,34,114]. In brief, in the yeast display deep mutational approach, yeast libraries expressing all possible amino acids substitutions in the RBD are incubated with either mAbs or polyclonal plasma, and then antibody escape cells are selected using fluorescence-activated cell sorting followed by deep sequencing to compute the escape fraction for each mutation. In other methods, a replication-competent chimeric vesicular stomatitis virus (VSV) encoding the SARS-CoV-2 spike protein is passaged in the presence of nAbs to select escape variants for each of the antibodies [30,33,34,114]. Weisblum and colleagues passaged rVSV/SARS-CoV-2 in presence of C121, C135, and C144 mAbs. In the case of C121, C135, and C144 antibodies, mutations E484K and Q493K/R, R346K/S/L and N440K, and E484 and Q493 were observed, respectively [30]. Greaney and colleagues used a yeast display system to gain a broad picture of viral escape by comprehensively mapping 22 different nAbs and polyclonal plasma targeting the RBD epitopes as discussed in the previous section [28]. The mutational antigenic profiling provides a comprehensive mutation-level scan of the functional binding epitopes between the RBD and nAbs. A comparison of the overlap between the structural epitopes and functional epitopes of the RBD-nAbs complexes lead to the following conclusion: Mutations that escape antibody binding are broadly located in or near the binding site on the RBD, and antibodies within the same class are escaped by mutations at similar sites in the RBD [28] (Fig 5). For example, neutralization by RBD-Cluster 2a antibodies is primarily affected by the K417N but hardly by the E484K mutation, and RBD-Cluster 2b antibodies are heavily affected by the E484K but less by the K417N mutation. However, RBD-3 antibodies are affected by both N501T/Y and E484K mutations [80]. Although class 1 and class 2 antibodies have significant overlap on their structural footprints (Fig 4B and 4J), escape mutants at K417, D420, N460, and S475 sites were observed for class 1 but not for class 2 antibodies. On the other hand, class 2 antibodies but not class 1 were escaped by mutations at sites L452R, E484, E490, and Q493, suggesting a functional diversity of antibodies despite having an overlap in their binding footprints (Fig 5A-5D). Class 3 antibodies were found to be escaped by mutations at R346, K444, and G446-450 sites [28] (Fig 5E and 5F). Of note, the antibody escape sites for HIV envelope protein were largely found outside the structural contact site, suggesting that an alteration of noncontact sites can also affect antibody sensitivity [26]. Notably, in the

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yeast display experiments, the isolated RBD was used; hence, they do not report comprehensively on the escape mutations at the quaternary binding sites on a trimeric spike protein.
Overall, a remarkable match is observed between the antibody escape map and antibody binding footprints on the RBD (Fig 5A, 5B, 5C, 5D, 5E, 5F, 5G, 5H, 5I and 5J pairs), with a few exceptions. Interestingly, these artificially generated antibody escape mutations are present in the naturally emerging virus populations. In particular, E484K mutation most strongly escapes the class 2 antibodies, including class 1 antibodies in certain cases, and also exists in the Beta, Gamma, Zeta (P.2), and B.1526 variants [25]. Of these, Beta and Gamma also harbor class 1 antibody escape mutation, K417N or K417T, respectively. The class 3 escape mutations are found in very few variants, one example being the L452R mutation present in the Epsilon (B.1.427/429) and variants of B.1.617 lineage. However, no viral variant so far has emerged with those mutations that escape all 3 antibody classes. Therefore, close monitoring of SARS-CoV-2 sequences is warranted because the development of a strain that can escape all 4 antibody classes would be a big burden to the ongoing public health and vaccine development efforts.

Conclusions
Francis Crick famously said, "if you want to understand the function, study structure". In the last more than a year, an unprecedented number of structures of the SARS-CoV-2 spike protein, including its variants, in complex with numerous mAbs have been determined to understand the molecular mechanism of antibody-mediated neutralization of SARS-CoV-2. The structural analyses of these complexes provide a comprehensive map of nAb epitopes on the spike protein. However, these analyses do not directly measure how/ which mutations will escape from antibody binding. Going forward, mutations in the RBD that escape antibody binding were identified by different methods [27,28,30,[32][33][34]114]. An analysis between the structural contact sites and escape maps suggested that these maps complement each other; therefore, comprehensive knowledge of immunodominant epitopes on the spike protein and escape mutations would aid efforts to understand viral evolution and rational design of antibody therapeutics, vaccines, and other countermeasures (Tables 1 and S1).
Antibodies that were isolated from the early COVID-19 phase were found to have a relatively low number of somatic mutations. However, it has been recently demonstrated that these antibodies show affinity maturation by somatic hypermutation in the lymphoid germinal centers, which empower them for increased binding affinity and neutralization potency for SARS-CoV-2 [84]. For example, C051 and C052 exhibit about 4-fold higher somatic hypermutation than the clonally related class 2 C144 antibody, and mutations in the RBD at L455, F456, F490, Q493, and S494 do not confer resistance anymore. These antibodies display an increased binding affinity for the RBD with Q493 mutation as compared to C144 but show resistance in binding to the RBD with E484K mutation [84]. It is important to note here that most of the affinity matured antibodies of class 2 were unable to neutralize SARS-CoV-2 pseudovirus with an E484K mutation alone or in combination with K417N and N501Y substitutions (B1.351 VOC) [84]. Overall, these results indicate that serological immunity is evolving to fight against the continuously evolving SARS-CoV-2 virus [84,115].
SARS-CoV-2 will continue to evolve, and it is nearly impossible to predict future variants; therefore, identification of bnAbs is a pressing need of the hour due to their strength of neutralizing multiple variants of a virus by recognizing evolutionarily conserved epitope. In this direction, the RBD-targeting antibodies, A23-58.1 and B1-182.1, were identified by Wang and colleagues, which neutralize multiple SARS-CoV-2 variants, including the B.1.1.7, B.1.351, P.1, and B.1.617 variants at subnanomolar concentration [116]. They bind to an invariant region of the RBD tip that is offset from major mutational hotspots (K417, E484, and N501), which increases their breadth and potency (Fig 6). These mutations are the major determinants conferring resistance in the B.1.1.7, B.1.351, P.1, and B.1.617 variants (Fig 2). The mAb 222 antibody is another notable example that binds both P.1 (K417T, E484K, and N501Y) and the ancestral Wuhan-Hu-1 RBD with similar affinities despite differences in the binding site. Notably, mAb 222, a Class 1 antibody, can neutralizes all 3 B.1.1.7, B.1.351, and P.1 variants despite its interactions with 2 of the ACE2-binding site mutations [60] (Fig 4E). The RBD-Fab 222 structure (PDB: 7NX6) indicates that the CDRH1 and CDRH2 weakly interact with K417N/T of the RBD, and CDRL1 contains a proline (residue P30) due to a rare somatic mutation that forms a cis-amide bond [89] with N501Y of the RBD [60] (Fig 4E). The 7D6 is a recently isolated bnAb that binds away from the RBM and is not sensitive to currently circulating SARS-CoV-2 variants. The crystal structure shows that 7D6 binds a novel cryptic site located behind the receptor-binding ridge of the RBD that faces toward the NTD. The 7D6 antibody binding causes interference with the adjacent NTD and appears to destabilize the spike protein. Structural analysis has shown that the 7D6 binding site residues are nevertheless conserved within the Sarbecovirus subgenus and the 7D6-epitope location is distinct from those bound by most antibodies that are insensitive to the mutations [117] (Fig 6C). These antibodies are classified as bnAbs based on the data available and can be further modified and evaluated for their use in cocktail therapy.
In addition to bnAbs, broadly neutralizing nanobodies are also identified that are capable of neutralizing B.1.1.7 (Alpha), B.1.351 (Beta), and P.1 (Gamma) variants [118]. Xu and colleagues identified 2 groups of neutralizing nanobodies from llama and an engineered mouse (nanomouse). Nanomouse nanobodies, Nb12 and Nb30, target a conserved region on the RBD that is largely inaccessible to human antibodies and is located outside the ACE2-binding motif (PDB: 7MY3 and 7MY2), which explains why their binding is not affected by E484K (Beta and Gamma) or N501Y (Alpha) substitutions [118]. Going forward with the identification of more effective therapies against SARS-CoV-2, multiple laboratories have reported the development of bispecific antibodies by combining 2 antibodies that target nonoverlapping epitopes on the spike protein and multivalent nanobodies. These engineered molecules have been described to be highly potent in neutralizing the SARS-CoV-2 variants and suppressing mutational escape [119][120][121][122]. Alongside this, antibodies from the NTD and community RBD-1 to RBD-4 are an attractive choice for the therapeutic cocktails being more potent than others, but the data suggest that emerging SARS-CoV-2 variants tend to escape binding by many members of the groups associated with most potent neutralizers [80,81]. Notably, the epitopes targeted by RBD-5 to RBD-7 antibodies are highly conserved but less potent in the Sarbecovirus subgenus of Betacoronavirus; therefore, they can be engineered in multivalent format to achieve enhanced potency and further use in the variant-resistant cocktails formulation [80]. For example, RBD-5 to RBD-7 or Class 4 antibodies, such as S2X259 (PDB: 7RA8 and 7RAL) [103] and DH1047 [104], are broadly protective antibodies, which bind to an epitope that is highly conserved among the Sarbecovirus subgenus. Although nAbs are an important defense against viral infections, they are not the only mechanism of protection. The T cells responses and non-nAbs are additional measures to protect from viral infections [123,124]. Pfizer-BioN-Tech and Moderna mRNA vaccines for SARS-CoV-2 have been shown to elicit cross-protective B and T cell responses, which can recognize different SARS-CoV-2 variants and are minimally affected by mutations in the spike protein [125][126][127][128]. This suggests that vaccineinduced immunity will continue to protect against currently circulating SARS-CoV-2 variants. The SARS-CoV-2 virus will continue to evolve, resulting in the emergence of escape variants; therefore, worldwide genomic surveillance, better vaccination drive, development of bnAbs, and new drugs are vital to combat COVID-19.
Supporting information S1

Acknowledgments
We thank Prof. Dr. Jonathan Coleman for critical reading the manuscript. . The RBD is shown in gray containing the RBM in cyan at their top. (B, C) S309 is a class 3 antibody while 7D6 binds proximal to the S309 epitope. S309 recognizes an epitope containing a glycan in white (N343 in SARS-CoV-2). 7D6 binds a novel cryptic site located behind the receptor-binding ridge of the RBD that faces toward the NTD. The S309 and 7D6 binding site residues are conserved within the Sarbecovirus subgenus. Both antibodies are resistant to mutations that emerged in the SARS-CoV-2 variants. The footprint residues on the RBD have been defined as those residues, which were within 4 Å of a Fab atom. bnAb, broadly neutralizing antibody; NTD, N-terminal domain; RBD, receptor-binding domain; RBM, receptor-binding motif; SARS-CoV-2, Severe Acute Respiratory Syndrome Coronavirus 2; VOC, variant of concern. https://doi.org/10.1371/journal.ppat.1010260.g006